data_1XDK # _model_server_result.job_id NEUbA0PKA8dBmZFwNqraYw _model_server_result.datetime_utc '2025-08-03 13:52:41' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1xdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":1500}' # _entry.id 1XDK # _exptl.entry_id 1XDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 300.435 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(9cis)-retinoic acid' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 1XDK _cell.length_a 115.7 _cell.length_b 115.7 _cell.length_c 247.2 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA octameric 8 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,M,N 1 1 E,F,G,H,K,L,O,P 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N # _chem_comp.formula 'C20 H28 O2' _chem_comp.formula_weight 300.435 _chem_comp.id 9CR _chem_comp.mon_nstd_flag . _chem_comp.name '(9cis)-retinoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O1 C15 9CR doub 1 n n C15 C14 9CR sing 2 n n C15 O2 9CR sing 3 n n C14 C13 9CR doub 4 e n C13 C12 9CR sing 5 n n C13 C20 9CR sing 6 n n C12 C11 9CR doub 7 e n C11 C10 9CR sing 8 n n C18 C5 9CR sing 9 n n C10 C9 9CR doub 10 z n C9 C19 9CR sing 11 n n C9 C8 9CR sing 12 n n C8 C7 9CR doub 13 e n C5 C4 9CR sing 14 n n C5 C6 9CR doub 15 n n C4 C3 9CR sing 16 n n C7 C6 9CR sing 17 n n C6 C1 9CR sing 18 n n C3 C2 9CR sing 19 n n C1 C17 9CR sing 20 n n C1 C2 9CR sing 21 n n C1 C16 9CR sing 22 n n C2 H1 9CR sing 23 n n C2 H2 9CR sing 24 n n C3 H3 9CR sing 25 n n C3 H4 9CR sing 26 n n C4 H5 9CR sing 27 n n C4 H6 9CR sing 28 n n C7 H7 9CR sing 29 n n C8 H8 9CR sing 30 n n C10 H9 9CR sing 31 n n C11 H10 9CR sing 32 n n C12 H11 9CR sing 33 n n C14 H12 9CR sing 34 n n C16 H13 9CR sing 35 n n C16 H14 9CR sing 36 n n C16 H15 9CR sing 37 n n C17 H16 9CR sing 38 n n C17 H17 9CR sing 39 n n C17 H18 9CR sing 40 n n C18 H19 9CR sing 41 n n C18 H20 9CR sing 42 n n C18 H21 9CR sing 43 n n C19 H22 9CR sing 44 n n C19 H23 9CR sing 45 n n C19 H24 9CR sing 46 n n C20 H25 9CR sing 47 n n C20 H26 9CR sing 48 n n C20 H27 9CR sing 49 n n O2 H28 9CR sing 50 n n # _atom_sites.entry_id 1XDK _atom_sites.fract_transf_matrix[1][1] 0.008643 _atom_sites.fract_transf_matrix[1][2] 0.00499 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00998 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004045 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code I 4 9CR A 1 500 500 9CR REA . J 4 9CR B 1 600 600 9CR REA . K 4 9CR E 1 1500 1500 9CR REA . L 4 9CR F 1 1600 1600 9CR REA . M 5 HOH A 1 701 701 HOH HOH . M 5 HOH A 2 704 704 HOH HOH . M 5 HOH A 3 705 705 HOH HOH . M 5 HOH A 4 706 706 HOH HOH . N 5 HOH B 1 702 702 HOH HOH . N 5 HOH B 2 703 703 HOH HOH . O 5 HOH E 1 707 707 HOH HOH . O 5 HOH E 2 710 710 HOH HOH . O 5 HOH E 3 711 711 HOH HOH . O 5 HOH E 4 712 712 HOH HOH . P 5 HOH F 1 708 708 HOH HOH . P 5 HOH F 2 709 709 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 9CR . . . K 4 39.633 24.386 123.726 1 51 ? C1 9CR 1500 E 1 HETATM 2 C C2 9CR . . . K 4 38.206 24.714 124.304 1 49.24 ? C2 9CR 1500 E 1 HETATM 3 C C3 9CR . . . K 4 37.356 23.559 124.837 1 48.86 ? C3 9CR 1500 E 1 HETATM 4 C C4 9CR . . . K 4 38.106 22.652 125.786 1 49.92 ? C4 9CR 1500 E 1 HETATM 5 C C5 9CR . . . K 4 39.632 22.477 125.561 1 51.11 ? C5 9CR 1500 E 1 HETATM 6 C C6 9CR . . . K 4 40.354 23.258 124.636 1 51.53 ? C6 9CR 1500 E 1 HETATM 7 C C7 9CR . . . K 4 41.806 23.076 124.426 1 54.31 ? C7 9CR 1500 E 1 HETATM 8 C C8 9CR . . . K 4 42.773 23.179 125.345 1 57.62 ? C8 9CR 1500 E 1 HETATM 9 C C9 9CR . . . K 4 44.15 22.992 125.328 1 58.48 ? C9 9CR 1500 E 1 HETATM 10 C C10 9CR . . . K 4 44.846 23.169 126.46 1 60.64 ? C10 9CR 1500 E 1 HETATM 11 C C11 9CR . . . K 4 44.475 23.574 127.818 1 64.01 ? C11 9CR 1500 E 1 HETATM 12 C C12 9CR . . . K 4 45.347 23.609 128.857 1 65.95 ? C12 9CR 1500 E 1 HETATM 13 C C13 9CR . . . K 4 44.967 24.025 130.245 1 67.31 ? C13 9CR 1500 E 1 HETATM 14 C C14 9CR . . . K 4 45.92 23.928 131.133 1 69 ? C14 9CR 1500 E 1 HETATM 15 C C15 9CR . . . K 4 46.009 24.172 132.596 1 69.18 ? C15 9CR 1500 E 1 HETATM 16 C C16 9CR . . . K 4 40.311 25.781 123.666 1 51.27 ? C16 9CR 1500 E 1 HETATM 17 C C17 9CR . . . K 4 39.474 23.9 122.291 1 49.5 ? C17 9CR 1500 E 1 HETATM 18 C C18 9CR . . . K 4 40.078 21.373 126.487 1 53.51 ? C18 9CR 1500 E 1 HETATM 19 C C19 9CR . . . K 4 44.814 22.559 124.049 1 60.25 ? C19 9CR 1500 E 1 HETATM 20 C C20 9CR . . . K 4 43.562 24.48 130.581 1 67.7 ? C20 9CR 1500 E 1 HETATM 21 O O1 9CR . . . K 4 45.371 25.124 133.182 1 71.22 ? O1 9CR 1500 E 1 HETATM 22 O O2 9CR . . . K 4 46.72 23.335 133.25 1 68.03 ? O2 9CR 1500 E 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #